diff macro.xml @ 3:e8405163fb4e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"

--- a/macro.xml	Thu Jan 02 12:03:50 2020 -0500
+++ b/macro.xml	Tue Aug 10 11:29:58 2021 +0000
@@ -1,40 +1,14 @@
 <?xml version="1.1"?>
 <macros>
+  <token name="@TOOL_VERSION@">0.10.0</token>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.7.0">mykrobe</requirement>
+      <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>
     </requirements>    
   </xml>
   <token name="@select_inputs@">
     <![CDATA[
          #set $name='sample'
-         #set $type='fastq'
-         ## Adding sample name, indicate specie and inputs fastq(s) files
-          #if $data_type.type == "paired":
-
-            ln -s '$data_type.fastq_input1' sample_1.fastq &&
-            ln -s '$data_type.fastq_input2' sample_2.fastq &&
-
-
-        #elif $data_type.type == "collection":
-            #set $name=str($data_type.fastq_input1.name)
-            ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq &&
-            ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq &&
-
-        #elif $data_type.type == "single":
-
-
-            #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
-              ln -s '$data_type.fastq_input1' sample.fastq &&
-
-            #end if
-
-            #if $data_type.fastq_input1.is_of_type('bam'):
-              ln -s '$data_type.fastq_input1' sample.bam &&
-              #set $type='bam'
-            #end if
-
-        #end if
     ]]>
   </token>
 
@@ -97,14 +71,14 @@
         <option value="collection">Collection Paired-end Data</option>
       </param>
       <when value="single">
-        <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/>
+        <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/>
       </when>
       <when value="paired">
-        <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
-        <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
+        <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>
+        <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>
       </when>
       <when value="collection">
-        <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
+        <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" />
       </when>
     </conditional>
   </xml>